Source code for large_image_source_vips

# -*- coding: utf-8 -*-

import math
import os
import threading
import uuid
from pathlib import Path

import cachetools
import numpy
import pyvips

from large_image import config
from large_image.cache_util import LruCacheMetaclass, methodcache
from large_image.constants import (NEW_IMAGE_PATH_FLAG, TILE_FORMAT_NUMPY,
                                   GValueToDtype, SourcePriority,
                                   dtypeToGValue)
from large_image.exceptions import TileSourceError, TileSourceFileNotFoundError
from large_image.tilesource import FileTileSource
from large_image.tilesource.utilities import _imageToNumpy

# Default to ignoring files with no extension and some specific extensions.
config.ConfigValues['source_vips_ignored_names'] = \
    r'(^[^.]*|\.(yml|yaml|json|png|svs))$'


[docs]class VipsFileTileSource(FileTileSource, metaclass=LruCacheMetaclass): """ Provides tile access to any libvips compatible file. """ cacheName = 'tilesource' name = 'vips' extensions = { None: SourcePriority.LOW, } mimeTypes = { None: SourcePriority.FALLBACK, } _tileSize = 256 def __init__(self, path, **kwargs): """ Initialize the tile class. See the base class for other available parameters. :param path: a filesystem path for the tile source. """ super().__init__(path, **kwargs) if str(path).startswith(NEW_IMAGE_PATH_FLAG): return self._initNew(**kwargs) self._largeImagePath = str(self._getLargeImagePath()) self._editable = False self._ignoreSourceNames('vips', self._largeImagePath) try: self._image = pyvips.Image.new_from_file(self._largeImagePath) except pyvips.error.Error: if not os.path.isfile(self._largeImagePath): raise TileSourceFileNotFoundError(self._largeImagePath) from None raise TileSourceError('File cannot be opened via pyvips') self.sizeX = self._image.width self.sizeY = self._image.height self.tileWidth = self.tileHeight = self._tileSize pages = 1 if 'n-pages' in self._image.get_fields(): pages = self._image.get('n-pages') self._frames = [0] for page in range(1, pages): subInputPath = self._largeImagePath + '[page=%d]' % page subImage = pyvips.Image.new_from_file(subInputPath) if subImage.width == self.sizeX and subImage.height == self.sizeY: self._frames.append(page) continue if subImage.width * subImage.height < self.sizeX * self.sizeY: continue self._frames = [page] self.sizeX = subImage.width self.sizeY = subImage.height self._image = subImage self.levels = int(max(1, math.ceil(math.log( float(max(self.sizeX, self.sizeY)) / self.tileWidth) / math.log(2)) + 1)) if len(self._frames) > 1: self._recentFrames = cachetools.LRUCache(maxsize=6) self._frameLock = threading.RLock() def _initNew(self, **kwargs): """ Initialize the tile class for creating a new image. """ self._largeImagePath = None self._image = None self.sizeX = self.sizeY = self.levels = 0 self.tileWidth = self.tileHeight = self._tileSize self._frames = [0] self._cacheValue = str(uuid.uuid4()) self._output = None self._editable = True self._bandRanges = None self._addLock = threading.RLock()
[docs] def getState(self): # Use the _cacheValue to avoid caching the source and tiles if we are # creating something new. if not hasattr(self, '_cacheValue'): return super().getState() return super().getState() + ',%s' % (self._cacheValue, )
[docs] def getInternalMetadata(self, **kwargs): """ Return additional known metadata about the tile source. Data returned from this method is not guaranteed to be in any particular format or have specific values. :returns: a dictionary of data or None. """ result = {} if not self._image: return result for key in self._image.get_fields(): try: result[key] = self._image.get(key) except Exception: pass if len(self._frames) > 1: result['frames'] = [] for idx in range(1, len(self._frames)): frameresult = {} result['frames'].append(frameresult) img = self._getFrameImage(idx) for key in img.get_fields(): try: frameresult[key] = img.get(key) except Exception: pass return result
[docs] def getMetadata(self): """ Return a dictionary of metadata containing levels, sizeX, sizeY, tileWidth, tileHeight, magnification, mm_x, mm_y, and frames. :returns: metadata dictionary. """ result = super().getMetadata() if len(self._frames) > 1: result['frames'] = [{} for _ in self._frames] self._addMetadataFrameInformation(result) return result
def _getFrameImage(self, frame=0): """ Get the vips image associated with a specific frame. :param frame: the 0-based frame to get. :returns: a vips image. """ if self._image is None and self._output: self._outputToImage() img = self._image if frame > 0: with self._frameLock: if frame not in self._recentFrames: subpath = self._largeImagePath + '[page=%d]' % self._frames[frame] img = pyvips.Image.new_from_file(subpath) self._recentFrames[frame] = img else: img = self._recentFrames[frame] return img
[docs] def getNativeMagnification(self): """ Get the magnification at a particular level. :return: magnification, width of a pixel in mm, height of a pixel in mm. """ return { 'mm_x': self.mm_x, 'mm_y': self.mm_y, 'magnification': 0.01 / self.mm_x if self.mm_x else None, }
[docs] @methodcache() def getTile(self, x, y, z, pilImageAllowed=False, numpyAllowed=False, **kwargs): frame = self._getFrame(**kwargs) self._xyzInRange(x, y, z, frame, len(self._frames)) img = self._getFrameImage(frame) x0, y0, x1, y1, step = self._xyzToCorners(x, y, z) tileimg = img.crop(x0, y0, x1 - x0, y1 - y0) tileimg = tileimg.reduce(step, step, kernel=pyvips.enums.Kernel.NEAREST) tile = numpy.ndarray( buffer=tileimg.write_to_memory(), dtype=GValueToDtype[tileimg.format], shape=[tileimg.height, tileimg.width, tileimg.bands]) return self._outputTile(tile, TILE_FORMAT_NUMPY, x, y, z, pilImageAllowed, numpyAllowed, **kwargs)
def _checkEditable(self): """ Raise an exception if this is not an editable image. """ if not self._editable: raise TileSourceError('Not an editable image') def _updateBandRanges(self, tile): """ Given a 3-d numpy array, update the tracked band ranges. :param tile: a numpy array. """ amin = numpy.amin(tile, axis=(0, 1)) amax = numpy.amax(tile, axis=(0, 1)) if self._bandRanges is None: self._bandRanges = { 'min': amin, 'max': amax, } else: delta = len(self._bandRanges['min']) - len(amin) if delta > 0: amin = numpy.array(list(amin) + [0] * delta) amax = numpy.array(list(amax) + [0] * delta) elif delta < 0: self._bandRanges['min'] = numpy.array(list(self._bandRanges['min']) + [0] * -delta) self._bandRanges['max'] = numpy.array(list(self._bandRanges['max']) + [0] * -delta) self._bandRanges = { 'min': numpy.minimum(self._bandRanges['min'], amin), 'max': numpy.maximum(self._bandRanges['max'], amax), } def _addVipsImage(self, vimg, x=0, y=0): """ Add a vips image to the output image. :param vimg: a vips image. :param x: location in destination for upper-left corner. :param y: location in destination for upper-left corner. """ # Allow vips to persist the new tile to a temp file. Otherwise, it may # try to hold all tiles in memory. vimgTemp = pyvips.Image.new_temp_file('%s.v') vimg.write(vimgTemp) vimg = vimgTemp with self._addLock: if self._output is None: self._output = { 'images': [], 'interp': vimg.interpretation, 'bands': vimg.bands, 'minx': None, 'miny': None, 'width': 0, 'height': 0, } self._output['images'].append({'image': vimg, 'x': x, 'y': y}) if (self._output['interp'] != vimg.interpretation and self._output['interp'] != pyvips.Interpretation.MULTIBAND): if vimg.interpretation in { pyvips.Interpretation.MULTIBAND, pyvips.Interpretation.RGB}: self._output['interp'] = vimg.interpretation if vimg.interpretation == pyvips.Interpretation.RGB and self._output['bands'] == 2: self._output['bands'] = 4 self._output['bands'] = max(self._output['bands'], vimg.bands) self._output['minx'] = min( self._output['minx'] if self._output['minx'] is not None else x, x) self._output['miny'] = min( self._output['miny'] if self._output['miny'] is not None else y, y) self._output['width'] = max(self._output['width'], x + vimg.width) self._output['height'] = max(self._output['height'], y + vimg.height) self._invalidateImage() def _invalidateImage(self): """ Invalidate the tile and class cache """ if self._output is not None: self._image = None w, h = self._output['width'], self._output['height'] w = max(self.minWidth or w, w) h = max(self.minHeight or h, h) self.sizeX = w self.sizeY = h self.levels = int(max(1, math.ceil(math.log( float(max(self.sizeX, self.sizeY)) / self.tileWidth) / math.log(2)) + 1)) self._cacheValue = str(uuid.uuid4())
[docs] def addTile(self, tile, x=0, y=0, mask=None, interpretation=None): """ Add a numpy or image tile to the image, expanding the image as needed to accommodate it. :param tile: a numpy array, PIL Image, vips image, or a binary string with an image. The numpy array can have 2 or 3 dimensions. :param x: location in destination for upper-left corner. :param y: location in destination for upper-left corner. :param mask: a 2-d numpy array (or 3-d if the last dimension is 1). If specified, areas where the mask is false will not be altered. :param interpretation: one of the pyvips.enums.Interpretation or 'L', 'LA', 'RGB', "RGBA'. This defaults to RGB/RGBA for 3/4 channel images and L/LA for 1/2 channels. The special value 'pixelmap' will convert a 1 channel integer to a 3 channel RGB map. For images which are not 1 or 3 bands with an optional alpha, specify MULTIBAND. In this case, the mask option cannot be used. """ self._checkEditable() if not isinstance(tile, pyvips.vimage.Image): tile, mode = _imageToNumpy(tile) interpretation = interpretation or mode with self._addLock: self._updateBandRanges(tile) if interpretation == 'pixelmap': with self._addLock: self._interpretation = 'pixelmap' tile = numpy.dstack(( (tile % 256).astype(int), (tile / 256).astype(int) % 256, (tile / 65536).astype(int) % 256)).astype('B') interpretation = pyvips.enums.Interpretation.RGB if interpretation != pyvips.Interpretation.MULTIBAND and tile.shape[2] in {1, 3}: newarr = numpy.zeros( (tile.shape[0], tile.shape[1], tile.shape[2] + 1), dtype=tile.dtype) newarr[:, :, :tile.shape[2]] = tile newarr[:, :, -1] = 255 tile = newarr if mask is not None: if len(mask.shape) == 3: mask = numpy.logical_or.reduce(mask, axis=2) if tile.shape[2] in {2, 4}: tile[:, :, -1] *= mask.astype(bool) else: raise TileSourceError('Cannot apply a mask if the source is not 1 or 3 channels.') if tile.dtype.char not in dtypeToGValue: tile = tile.astype(float) vimg = pyvips.Image.new_from_memory( numpy.ascontiguousarray(tile).data, tile.shape[1], tile.shape[0], tile.shape[2], dtypeToGValue[tile.dtype.char]) interpretation = interpretation if any( v == interpretation for k, v in pyvips.enums.Interpretation.__dict__.items() if not k.startswith('_')) else ( pyvips.Interpretation.B_W if tile.shape[2] <= 2 else ( pyvips.Interpretation.RGB if tile.shape[2] <= 4 else pyvips.Interpretation.MULTIBAND)) vimg = vimg.copy(interpretation=interpretation) # The alpha channel is [0, 255] if we created it (which is true if the # band range doesn't include it) self._addVipsImage(vimg, x, y)
def _getVipsFormat(self): """ Get the recommended vips format for the output image based on the band range and the interpretation. :returns: a vips BandFormat. """ bmin, bmax = min(self._bandRanges['min']), max(self._bandRanges['max']) if getattr(self, '_interpretation', None) == 'pixelmap': format = pyvips.enums.BandFormat.UCHAR elif bmin >= -1 and bmax <= 1: format = pyvips.enums.BandFormat.FLOAT elif bmin >= 0 and bmax < 2 ** 8: format = pyvips.enums.BandFormat.UCHAR elif bmin >= 0 and bmax < 2 ** 16: format = pyvips.enums.BandFormat.USHORT elif bmin >= 0 and bmax < 2 ** 32: format = pyvips.enums.BandFormat.UINT elif bmin < 0 and bmin >= -(2 ** 7) and bmax < 2 ** 7: format = pyvips.enums.BandFormat.CHAR elif bmin < 0 and bmin >= -(2 ** 15) and bmax < 2 ** 15: format = pyvips.enums.BandFormat.SHORT elif bmin < 0 and bmin >= -(2 ** 31) and bmax < 2 ** 31: format = pyvips.enums.BandFormat.INT else: format = pyvips.enums.BandFormat.FLOAT return format def _outputToImage(self): """ Create a vips image that pipelines all of the pieces we have into a single image. This makes an image that is large enough to hold all of the pieces and is an appropriate datatype to represent the range of values that are present. For pixelmaps, this will be RGB 8-bit. An alpha channel is always included unless the intrepretation is multichannel. """ with self._addLock: bands = self._output['bands'] if bands in {1, 3}: bands += 1 img = pyvips.Image.black(self.sizeX, self.sizeY, bands=bands) if self.mm_x or self.mm_y: img = img.copy( xres=1.0 / (self.mm_x if self.mm_x else self._mm_y), yres=1.0 / (self.mm_y if self.mm_y else self._mm_x)) format = self._getVipsFormat() if img.format != format: img = img.cast(format) baseimg = img.copy(interpretation=self._output['interp'], format=format) leaves = math.ceil(len(self._output['images']) ** (1. / 3)) img = baseimg.copy() trunk = baseimg.copy() branch = baseimg.copy() for idx, entry in enumerate(self._output['images']): branch = branch.composite( entry['image'], pyvips.BlendMode.OVER, x=entry['x'], y=entry['y']) if not ((idx + 1) % leaves) or idx + 1 == len(self._output['images']): trunk = trunk.composite(branch, pyvips.BlendMode.OVER, x=0, y=0) branch = baseimg.copy() if not ((idx + 1) % (leaves * leaves)) or idx + 1 == len(self._output['images']): img = img.composite(trunk, pyvips.BlendMode.OVER, x=0, y=0) trunk = baseimg.copy() self._image = img
[docs] def write(self, path, lossy=True, alpha=True, overwriteAllowed=True, vips_kwargs=None): """ Output the current image to a file. :param path: output path. :param lossy: if false, emit a lossless file. :param alpha: True if an alpha channel is allowed. :param overwriteAllowed: if False, raise an exception if the output path exists. :param vips_kwargs: if not None, save the image using these kwargs to the write_to_file function instead of the automatically chosen ones. In this case, lossy is ignored and all vips options must be manually specified. """ if not overwriteAllowed and os.path.exists(path): raise TileSourceError('Output path exists (%s)' % str(path)) with self._addLock: img = self._getFrameImage(0) # TODO: set image description: e.g., # img.set_type( # pyvips.GValue.gstr_type, 'image-description', # json.dumps(dict(vars(opts), indexCount=found))) if getattr(self, '_interpretation', None) == 'pixelmap': img = img[:3] elif (not alpha and getattr(self, '_output', {}).get( 'interp') != pyvips.Interpretation.MULTIBAND): img = img[:-1] if self.crop: x, y, w, h = self._crop w = max(0, min(img.width - x, w)) h = max(0, min(img.height - y, h)) x = min(x, img.width) y = min(y, img.height) img = img.crop(x, y, w, h) pathIsTiff = Path(path).suffix.lower() in {'.tif', '.tiff'} pixels = img.width * img.height if vips_kwargs is not None or not pathIsTiff: img.write_to_file(path, **(vips_kwargs or {})) elif not lossy: img.write_to_file( path, tile_width=self.tileWidth, tile_height=self.tileHeight, tile=True, pyramid=True, bigtiff=pixels >= 2 * 1024 ** 3, region_shrink='nearest', compression='lzw', predictor='horizontal') else: img.write_to_file( path, tile_width=self.tileWidth, tile_height=self.tileHeight, tile=True, pyramid=True, bigtiff=pixels >= 2 * 1024 ** 3, compression='jpeg', Q=90)
@property def crop(self): """ Crop only applies to the output file, not the internal data access. It consists of x, y, w, h in pixels. """ return getattr(self, '_crop', None) @crop.setter def crop(self, value): self._checkEditable() if value is None: self._crop = None return x, y, w, h = value x = int(x) y = int(y) w = int(w) h = int(h) if x < 0 or y < 0 or w <= 0 or h <= 0: raise TileSourceError('Crop must have non-negative x, y and positive w, h') self._crop = (x, y, w, h) @property def minWidth(self): return getattr(self, '_minWidth', None) @minWidth.setter def minWidth(self, value): self._checkEditable() value = int(value) if value is not None else None if value is not None and value <= 0: raise TileSourceError('minWidth must be positive or None') if value != getattr(self, '_minWidth', None): self._minWidth = value self._invalidateImage() @property def minHeight(self): return getattr(self, '_minHeight', None) @minHeight.setter def minHeight(self, value): self._checkEditable() value = int(value) if value is not None else None if value is not None and value <= 0: raise TileSourceError('minHeight must be positive or None') if value != getattr(self, '_minHeight', None): self._minHeight = value self._invalidateImage() @property def mm_x(self): if getattr(self, '_mm_x', None): return self._mm_x xres = 0 if self._image: xres = self._image.get('xres') or 0 return 1.0 / xres if xres else None @mm_x.setter def mm_x(self, value): self._checkEditable() value = float(value) if value is not None else None if value is not None and value <= 0: raise TileSourceError('mm_x must be positive or None') if value != getattr(self, '_minHeight', None): self._mm_x = value self._invalidateImage() @property def mm_y(self): if getattr(self, '_mm_y', None): return self._mm_y yres = 0 if self._image: yres = self._image.get('yres') or 0 return 1.0 / yres if yres else None @mm_y.setter def mm_y(self, value): self._checkEditable() value = float(value) if value is not None else None if value is not None and value <= 0: raise TileSourceError('mm_y must be positive or None') if value != getattr(self, '_minHeight', None): self._mm_y = value self._invalidateImage() @property def bandRanges(self): return getattr(self, '_bandRanges', None) @property def bandFormat(self): if not self._editable: return self._image.format return self._getVipsFormat()
# TODO: specify bit depth / bandFormat explicitly
[docs]def open(*args, **kwargs): """Create an instance of the module class.""" return VipsFileTileSource(*args, **kwargs)
[docs]def canRead(*args, **kwargs): """Check if an input can be read by the module class.""" return VipsFileTileSource.canRead(*args, **kwargs)
[docs]def new(*args, **kwargs): """ Create a new image, collecting the results from patches of numpy arrays or smaller images. """ return VipsFileTileSource(NEW_IMAGE_PATH_FLAG + str(uuid.uuid4()), *args, **kwargs)